Protein-Protein Interactions
The majority of biological processes in living organisms are mediated by proteins and their interactions with specific ligands e.g., other proteins, antigens, antibodies, nucleic acids, lipids and carbohydrates. Not only are such interactions involved in normal biological processes, protein interactions are also causative of processes involved in diseases or disorders. As a consequence, protein interactions are important targets for the development of new therapeutic compounds.
CD40 Ligand (CD40L or CD154) and CD40L Signaling Effects
CD40 ligand is a trimeric, transmembrane protein of the tumor necrosis factor family. A large variety of immunologic and vascular cells have been found to express CD40, CD40 ligand, or both.
For example, the CD40 ligand (CD40L or CD154), which is not expressed on resting human T cells, is up-regulated on the T-cell surface in response to foreign antigen presentation on MHC-class II molecules, up-regulation of the B7 antigen on the B-cell surface, formation of a complex between T-cells and B-cells via the T-cell receptor (TCR), and antigen recognition. Stimulation through the TCR also activates the T-cells, initiating T-cell cytokine production, interaction between the CD28 antigen on T-cells and the B7 antigen on B cells and binding of CD40L to CD40 receptor on the B-cell surface to thereby stimulate the B-cell to mature into a plasma cell secreting immunoglobulin.
The interaction between CD40L and the CD40 receptor may also cause adverse effects and transformed cells from patients with low-grade and high-grade B-cell lymphomas, B-cell acute lymphoblastic leukemia, multiple myeloma, chronic lymphocytic leukemia, and Hodgkin's disease express CD40. CD40 expression is also detected in two-thirds of acute myeloblastic leukemia cases and 50% of AIDS-related lymphomas. Immunoblastic B-cell lymphomas frequently arise in immune-compromized individuals such as allograft recipients and others receiving long-term immunosuppressive therapy, AIDS patients, and patients with primary immunodeficiency syndromes such as X-linked lymphoproliferative syndrome or Wiscott-Aldrich syndrome (Thomas et al., Adv. Cancer Res. 57, 329 (1991); Straus et al., Ann. Intern. Med. 118, 45 (1993). Malignant B cells from several tumors of B-cell lineage express a high degree of CD40 and appear to depend on CD40 signaling for survival and proliferation.
CD40-CD40L interactions may also promote immune-mediated angiogenesis, gut inflammation, acute intestinal injury or chronic intestinal injury, in the pathogenesis of inflammatory bowel disease (IBD). For example, the engagement of CD40L-activated HIF supernatants induce angiogenic events as determined by migration of HUMECs and tubule formation, both of which are inhibited using antibodies that bind to vascular endothelial growth factor (VEGF), interleukin-8 (IL-8) or hepatocyte growth factor (HGF). Additionally, CD40-deficient and CD40L-deficient mice are protected from DSS-induced colitis and display significant impairment of gut inflammation-driven angiogenesis, as determined by their microvascular density (Danese et al., Gut 56, 1248-1256, 2007).
CD40-CD40L interaction also activates extracellular signal-regulated kinase ½ and nuclear factor-KB pathways in insulinoma NIT-1 cells, and inhibitors of either pathway suppress cytokine/chemokine production in islets and up-regulate intercellular adhesion molecule-1 associated with inflammation, contributing to early islet graft loss after transplantation (Barbé-Tuana et al., Diabetes 55, 2437-2445, 2006).
Cell types typically resident in atherosclerotic plaques e.g., endothelial cells, macrophages and smooth muscle cells also express CD40L, and exposure to CD40L stimulates a broad inflammatory response in these cells such as heightened expression of pro-inflammatory cytokines, adhesion molecules, matrix degrading enzymes, and pro-coagulants, thereby leading to atherogenesis and lesion complication (Alderson et al., J Exp Med. 178, 669-674, 1993; Mach et al., Proc. Natl. Acad. Sci. USA 94, 1931-1936, 1997; Schonbeck et al., Circ Res. 89, 1092-1103, 2001; Mach et al., Nature 394, 200-203, 1998; Bavendiek et al., Arterioscler Thromb Vasc Biol. 25, 1244-1249, 2005). Animals that are deficient in CD40L have reduced levels of atherosclerosis on high-cholesterol diets and atherosclerotic lesions in such animals display features associated with plaque stability e.g., reduced macrophage count, reduced lipid content, increased collagen content (Lutgens et al., Nat. Med. 5, 1313-1316, 1999; Schonbeck et al., Proc. Natl. Acad. Sci. USA 97, 7458-7463, 2000). The soluble 18 kDa CD40L protein released from platelets on platelet activation may identify first or recurrent cardiovascular events, which further supports the pathogenic role of CD40L (Heeschen et al., N. Engl. J. Med. 348, 1104-1111, 2003; Schonbeck et al., Circulation 104, 2266-2268, 2001; Varo et al., Circulation 107, 2664-2669, 2003). Recently, Zirlik et al., Circulation 115, 1571-1580, 2007 demonstrated that CD40L interacts with Mac-1 on monocytes, and functionally enhances Mac-1 dependent monocyte adhesion and migration in vitro, and that inhibition of Mac-1 in vivo in LDLR−/− mice slows lesion development and macrophage accumulation in atherosclerotic plaques. Zirlik et al. suggest that the CD40L-Mac-1 interaction may participate, albeit not necessarily exclusively, in the expression of several pro-inflammatory cytokines including MIP-2, interleukin-1β, IL-8, pro-coagulant tissue factor, and in the activation of pro-inflammatory NF-κB. Thus, CD40L not only may attract inflammatory cells via Mac-1, but also induces the expression of a variety of pro-inflammatory and pro-oxidant functions that promote atherogenesis.
Elevated soluble CD40L is also prognostic of an increased risk of thrombosis and cardiac ischemia.
Modulators of Protein-Protein Interactions
To identify suitable therapeutic compounds, the pharmaceutical industry has particularly focussed on screening processes to identify antibodies, peptides and small molecule compounds capable of interacting with a protein and/or inhibiting a protein interaction. To function as a drug suitable for administration to a subject an antibody, peptide or small molecule must be capable of binding to a target with high affinity and selectivity.
Peptides offer significant advantages over antibodies in terms of uptake and low immunogenicity, and over small molecules in terms of reduced toxicity.
1. Molecular Shape Considerations
Often, small molecules and short peptides do not effectively modulate protein interactions because they do not generally possess a required shape e.g., to fit into complex protein surfaces or bind to relatively featureless interfaces. As a consequence, small-molecules ands short peptides are generally unable to bind to many surfaces of a target protein with sufficiently-high affinity and specificity to modulate binding of a ligand to the target, or to otherwise agonize or antagonize the activity of the target protein. Accordingly, there is a high attrition rate for the screening of such molecules as drug leads for therapeutic applications, particularly for targets such as protein interactions.
2. Random Peptides
By way of example, notwithstanding that short random peptides e.g., peptide aptamers, may be sufficiently small for commercial i.e., large-scale production by chemical synthesis, they generally provide highly-variable bioactivities against target proteins, and interactions with their targets are generally low affinity interactions. For example, in a screen of a random peptide library to identify a peptide capable of dissociating HIV protease fewer than about 1×10-6 peptides displayed the desired activity (Park and Raines Nat. Biotechnol., 18: 548-550, 2000). This low “hit” rate appears to be a result of the inability of the such random peptides to assume stable secondary structure and/or tertiary structure to thereby facilitate binding to a target protein.
3. Structural Constraint
In response to the low “hit” rate for identifying new drug leads, the pharmaceutical industry has expended some effort in developing synthetic scaffolds for presenting ligands to proteins, with a view to modulating activity of the target protein. However, such constraint of random peptide libraries has failed to increase the “hit” rate for identifying new drug candidates based on random peptide sequences to a level that makes peptides a viable alternative to small molecules. For example, random peptides have been constrained within scaffold structures e.g., the active site loop of thioredoxin (“Trx”; Colas et al., Nature, 380: 548-550, 1996) and tested for binding to cyclin-dependent kinase-2 (Cdk-2), however fewer than 2×10-5 of the Trx-constrained peptides actually blocked the target. Thus, the provision of synthetic scaffolds does not necessarily enhance “hit” rate. It is also possible that the limited repertoire of artificial scaffolds available to the industry will necessarily limit the diversity of structures that can be produced using such approaches, and may even mask or modify any native structures formed.
4. Secondary Structures, Domains, Sub-Domains and Folds
Native proteins have considerable structural features, including protein “domains” that are generally of functional significance. Until the present invention, such structural features have largely been utilized to determine evolutionary relationships between proteins, and for dissecting dynamic folding pathways i.e., how particular proteins fold. For example, the CATH database (Orengo et al., Structure 5, 1093-1108, 1997) classifies proteins according to a hierarchy of Class, Architecture, Topology and Homologous superfamily based upon structure, sequence, and functional considerations. In particular, the CATH hierarchy acknowledges three basic structural features i.e., class, architecture and topology. Protein “class” is highest in the CATH hierarchy and, in this context is a reference to the secondary structure composition and packing of a protein i.e., mainly α-helix, mainly β-strand, and α−β including alternating a/β in which the secondary structures alternate along the protein chain, and α+β in which the α and β regions are largely segregated. Thus, the “class” to which a protein belongs is a global assignment based on secondary structure considerations. Protein “architecture” refers to the overall shape of a protein based upon groups of similar secondary structural arrangements irrespective of the order in which they are connected in the protein. Protein “topology” describes the relative associations and orientations of secondary structures in 3D and the order in which they are connected. Protein “folds” are recognized in the CATH hierarchy as a function of topology, however the literature is confusing in this respect, because a fold can adopt a specific architecture e.g., Orengo and Thornton, Ann. Rev. Biochem. 74, 867-900, 2005.
As used herein, the term “fold” is therefore taken in its broadest context to mean a tertiary structure formed by the folding of multiple secondary structures including aspects of both architecture and topology. Herein, the term “subdomain” is used interchangeably with the term “fold”. A “fold” may form independently or in association with other parts of a protein or other proteins or a scaffold structure.
Table 1 herein includes descriptions of segments of proteins comprising protein domains.
TABLE 1Exemplary structures adopted by homologous superfamilies of proteinsStructureArchitecture and/or topology of folds within proteinsα-helixα-helices; folded leaf, partly openedα-helix2α-helices; antiparallel hairpin, left-handed twistα-helixtandem repeat of two calcium-binding loop-helix motifs comprising α--helicesα-helixhelix-extended loop-helix; parallel α-helicesα-helix2α-helices: one short, one long; aromatic-rich interfaceα-helix3α-helices; folded leaf, openedα-helix3-α-helices; bundle, closed or partly opened, right-handed twist; up-and downα-helix3-α-helices; bundle, closed or partly opened, right-handed twist; up-and downα-helix3α-helices; bundle, right-handed twistα-helix3-4α-helicesα-helix3α-helices; architecture is similar to that of the “winged helix” foldα-helix3α-helices; bundle, closed, left-handed twist; up-and-downα-helix3α-helices; bundle, closed, left-handed twist; up-and-down; mirror topology tothe spectrin-like foldα-helix3α-helices; bundle, closed, right-handed twist; up-and-downα-helix3α-helices; bundle, closed, left-handed twist, up-and-downα-helixcore: 3α-helices; bundle, closed, left-handed twist; up-and-downα-helix3α-helices; bundle, partly openedα-helix3α-helices, the first one is shorter than the other two; bundle, partly openedα-helix3 short α-helices; irregular arrayα-helix3 short α-helices; irregular arrayα-helix3α-helices; irregular arrayα-helix3α-helices; irregular array; disulfide-richα-helixα-helices; irregular array; disulfide-richα-helix3α-helices; irregular arrayα-helix3α-helices; bundle, closed, right-handed twist; up-and-downα-helix3α-helices; bundle, closed, left-handed twist; parallelα-helix3α-helices; irregular arrayα-helix3α-helices; long middle helix is flanked at each end with shorter onesα-helix3α-helices; bundle, openα-helixα-helices; irregular arrayα-helix4α-helices; bundle, closed or partly opened, left-handed twist; up-and-downα-helix4α-helices; bundle, closed, right-handed twist; 1 crossover connectionα-helix4α-helices; bundle, closed, left-handed twist; 1 crossover connectionα-helix4α-helices; bundle, closed; left-handed twist; 2 crossover connectionsα-helix4α-helices; bundle; one loop crosses over one side of the bundleα-helix4α-helices, bundle; helix 3 is shorter than others; up-and-downα-helix4α-helices; bundle; minor mirror variant of up-and-down topologyα-helix4α-helices; dimer of identical alpha-hairpin subunits; bundle, closed, left-handedtwistα-helix4α-helices; bundle, closed, right-handed twistα-helix4α-helices; bundle, closed, right-handed twistα-helix4α-helices; bundle, closed, right-handed twistα-helix4α-helices; bundle, closed, left-handed twistα-helix4α-helices; bundle, closed, right-handed twistα-helix4α-helices; folded leaf, closedα-helix4α-helices; orthogonal arrayα-helix4α-helices; the long C-terminal helix protrudes from the domain and binds toDNAα-helix4-α-helices; bundle, closed, left-handed twist; 2 crossover connectionsα-helix4α-helices; array of 2 hairpins, openedα-helix4α-helices: bundleα-helix4α-helices: bundleα-helix4α-helices: open bundle; capped by two small 3-stranded beta-sheetsduplication: consists of two structural repeatsα-helix4α-helices: bundle; flanked by two short beta-hairpins duplication: consists oftwo structural repeatsα-helix4α-helices; array of 2 hairpins, openedα-helix4 helices; bundle, closed, left-handed twist; right-handed super helixα-helix4α-helices; bundle, left-handed twist; right-handed super helixα-helix4α-helices; bundle, right-handed twist; right-handed super helixα-helix4 long α-helices; bundle, left-handed twist (coiled coil); right-handed super helixα-helix4α-helices; bundle, left-handed twist; left-handed super helixα-helix4α-helices; bundle, right-handed twist; left-handed super helixα-helix4α-helices; irregular arrayα-helix2α-helices and adjacent loopsα-helix4α-helices; irregular arrayα-helix4α-helices; irregular arrayα-helix4α-helices; irregular array, disulfide-linkedα-helix4α-helices irregular array, disulfide-linkedα-helix4α-helices; irregular array, disulfide-linkedα-helix4α-helices; folded leaf; right-handed super helixα-helix4α-helices; folded leaf; right-handed super helixα-helix4α-helices; bundleα-helix4 long α-helices; bundleα-helix4 helices; bundle, partly openedα-helixcore: 4α-helices; bundle, partly opened, capped with a beta-sheetα-helix4α-helices, bundleα-helix4 helices; the three last helices form a bundle similar to that of the RuvA C-domainα-helix4α-helices; an orthogonal arrayα-helix4α-helices; an orthogonal arrayα-helix4α-helices; up-and-down bundleα-helix4α-helices; open up-and-down bundle; binds alpha-helical peptidesα-helix4α-helices; open up-and-down bundle; flexible N-terminal tailα-helix4α-helices; arrayα-helix4α-helices; bundle, closed, left-handed twistα-helix4α-helices dimer of identical alpha-hairpin subunits; open bundleα-helix4-5α-helices; bundle of two orthogonally packed alpha-hairpinsα-helix4-5α-helices; right-handed super helixα-helix5α-helices; right-handed super helix; swapped dimer with the two long C-terminal helicesα-helixα-helices array; two long helices form a hairpin that dimerizes into a 4-helicalbundleα-helix5α-helices; bundle, closed, left-handed twistα-helix5α-helices; bundle, closed, left-handed twistα-helix5α-helices; bundle, closed, left-handed twist; helices 2-5 adopt the Four-helicalup-and-down bundle foldα-helix5α-helices; bundle, closed, left-handed twistα-helix5α-helices; folded leaf, closedα-helix5α-helices; folded leaf, closedα-helix5α-helices; folded leafα-helix5α-helices; irregular array; left-handed super helixα-helix4-5α-helices; bundle; left-handed super helixα-helix5α-helices; bundleα-helix5α-helices; bundleα-helixα-helices; bundleα-helix5α-helices; bundleα-helixα-helices; one helix is surrounded by the othersα-helix5α-helices; one helix is surrounded by the othersα-helix5α-helices; one helix is surrounded by the othersα-helix5α-helices; contains one more helix and a beta-hairpin outside the coreα-helix5α-helices: bundleα-helixα-helical bundle; up-and-down; right-handed twistα-helix5α-helices: orthogonal arrayα-helix5α-helices: orthogonal arrayα-helix5α-helices: irregular arrayα-helix5α-helices; arrayα-helix5α-helices; orthogonal array; folding similarity to the TipA-S domainα-helix5α-helices; arrayα-helix6α-helices: bundle; left-handed twist, up-and-down topologyα-helix6α-helices, homodimer of 3-helical domainsα-helix6α-helices, homodimer of 3-helical domainsα-helix6α-helices, homodimer of 3-helical domainsα-helix6α-helices, heterodimer of 3-helical domainsα-helixdimer of 3α-helical segments; consists of two subdomains: 4-helical bundle andcoiled coilα-helix6α-helices: closed bundle; greek-key; internal pseudo twofold symmetryα-helix6α-helices: closed bundle; greek-key; internal pseudo twofold symmetryα-helix6α-helices: bundle; one central helix is surrounded by 5 othersα-helix6α-helices; bundle; one central helix is surrounded by 5 othersα-helix6α-helices: arrayα-helix6α-helices: orthogonal arrayα-helixirregular array of 6 short α-helicesα-helix6α-helices; one central helix is surrounded by 5 othersα-helix6α-helices; one central helix is surrounded by 5 othersα-helix6α-helices; bundle; one central helix is surrounded by 5 othersα-helixMultiple α-helicesα-helixMultihelical; core: 5-helical bundleα-helixmultihelical; contains compact array of 6 short helicesα-helixmultihelical; irregular array of long and short helicesα-helixmultihelical; irregular array of long and short helicesα-helixmultihelical bundle; contains buried central helixα-helixmultihelical; contains two buried central helicesα-helixmultihelical; can be divided into two subdomainsα-helixmultihelical; consists of two all-alpha subdomainscontains a 4-helical bundle with left-handed twist and up-and-down topologyα-helixmultihelical; consists of two all-alpha subdomains each containing a 3-helicalbundle with right-handed twistα-helixmultihelical; consists of two all-alpha subdomains; contains a 4-helical bundlewith left-handed twist and up-and-down topologyα-helixmultihelical; consists of two tightly associated 3-helical bundles with differenttwistsα-helixmultihelical; consists of two all-alpha subdomains; dimerα-helixmultihelical; consists of two all-alpha subdomainsA-helixmultihelical; consists of two all-alpha domainsA-helixmultihelical; consists of two different 3-helical domains connected by a long,partly helical linkerα-helixmultihelical; consists of two different alpha-helical bundles (4-helical and 3-helical)α-helixmultihelical; consists of two different alpha-helical bundlesα-helixmultihelical; consists of two different alpha-helical bundlesα-helixmultihelical; consists of two different all-alpha subdomains, 4 helices eachα-helixmultihelical; consists of two all-alpha domainsα-helixmultihelical; consists of two all-alpha domainsα-helixmultihelical; consists of two all-alpha subdomainsα-helixmultihelical consists of two all-alpha subdomainssubdomain 1 (residues 10-100) is a 4-helical bundleα-helixmultihelicalα-helixmultihelical; consists of two all-alpha subdomainsα-helixmultihelical; common core is formed around two long antiparallel helices relatedby (pseudo) twofold symmetryα-helixmultihelicalα-helixmultihelical; up to seven alpha-hairpins are arranged in closed circular arrayα-helixmultihelical; consists of two all-alpha domainsα-helixmultihelicalα-helixmultihelical; forms intertwined dimer of identical 5-helical subunitsα-helixmultihelical; intertwined tetramerα-helixmultihelical; intertwined trimer of identical 3-helical subunitsα-helixmultihelical; consists of two all-alpha domainsα-helixmultihelical; core: 5-helical bundle; binds cofactor at the beginning of third helixα-helixmultihelical; contains a 3-helical bundle surrounded by several shorter helicesα-helixmultihelical; contains a 3-helical Hin recombinase-like subdomain and two longdimerisation helicesα-helixmultihelical oligomeric proteinα-helixmultihelical; consists of a conserved 4-helical core and a variable insertsubdomainα-helixmultihelical; consists of 2 all-alpha subdomainsα-helixmultihelical; consists of 2 all-alpha subdomains, “rigid” one and “mobile” oneα-helixmultihelical; consists of 2 all-alpha subdomains connected by a long helixα-helixmultihelical; array of longer and shorter helices; contains an alpha-hairpindimerisation subdomainα-helixmultihelical; bundle of longer and shorter helicesα-helixmultihelical; three-helical bundle in the core is surrounded by non-conservedhelicesα-helixmultihelical; consists of two subdomainsα-helixmultihelicalα-helixmultihelicalα-helixmultihelical; can be divided into an alpha-alpha super helix domain and a longalpha-hairpin dimerization domainα-helixmultihelical; can be divided into three subdomains (neck, body and tail)α-helixmultihelical; 2 (curved) layers: alpha/alpha; right-handed super helixα-helixmultihelicalα-helixmultihelical; consists of two all-alpha subdomainsα-helixmultihelical; interlocked (homo)dimerα-helixmultihelical; interlocked heterodimer with F-box proteinsα-helixmultihelical; interlocked heterodimer with the Skp1 dimerisation domainα-helixmultihelical; 3 layers or orthogonally packed helicesα-helixmultihelicalα-helixmultihelical; consist of two subdomainsα-helixmultihelical; open arrayα-helixmultihelical; 2 layers or orthogonally packed helicesα-helixmultihelical bundle; contains buried central helixα-helixmultihelical; consists of two topologically similar alpha-helical bundlesα-helixmultihelical; consists of 2 four-helical bundlesα-helixmultihelical; one domain consists of two similar disulfide-linked subdomainsα-helixmultihelical, consists of three all-alpha domainsα-helixmultihelical, consists of three all-alpha domainsα-helixmultihelical; core: 8 helices (C-J) are arranged in 2 parallel layersα-helixmultihelical; 8 helices arranged in 2 parallel layersα-helixmultihelical; bundleα-helixmultihelical; core: 6 helices, bundleα-helixmultihelical; forms a boat-shaped protein shell around cofactorsα-helixmultihelical; bundleα-helixmultihelical; contains 4-helical bundle and 2-helical armα-helixmultihelical; arrayα-helixmultihelical; arrayα-helixmultihelical; bundleα-helixmultihelical; bundleα-helixmultihelical; bundleα-helixmultihelical; arrayα-helixcommon core: 2 helices, disulfide-linked, and a calcium-binding loopα-helix5 helices: irregular disulfide-linked array; also contains a small beta-hairpinα-helix5 helices: irregular disulfide-linked array; form homodimerα-helix5 helices: irregular disulfide-linked array; topological similarity to the Fungalelicitin foldα-helix6 helices: irregular non-globular array; also contains two small b-hairpinsα-helix3 helices, non-globular array; forms interlocked heterodimers with its targetsα-helixvariable number of helices and little beta structureβ-sheetsandwich; 7 strands in 2 sheets; greek-keyβ-sheetsandwich; 9 strands in 2 sheet; greek-key; subclass of immunoglobin-like foldβ-sheetsandwich; 7 strands in 2 sheets, greek-keyβ-sheetsandwich; 6 strands in 2 sheetsβ-sheetsandwich; 6 strands in 2 sheetsβ-sheetsandwich; 6 strands in 2 sheetsβ-sheetsix-stranded beta-sandwich, jelly-roll/greek-key topologyβ-sheetsandwich; 7 strands in 2 sheets, greek-keyβ-sheetsandwich; 7 strands in 2 sheets, greek-key; permutation of the immunoglobulin-like foldβ-sheetsandwich; 8 strands in 2 sheets; greek-keyβ-sheetsandwich; 8 strands in 2 sheets; greek-keyβ-sheetsandwich; 8 strands in 2 sheets; meanderβ-sheetsandwich; 8 strands in 2 sheets; meanderβ-sheetsandwich; 8 strands in 2 sheets; jelly-roll; some members can have additional 1-2strandsβ-sheetsandwich; 8 strands in 2 sheets; greek-keyβ-sheetsandwich; 8 strands in 2 sheets; complex topologyβ-sheetsandwich; 8 strands in 2 sheets; jelly-rollβ-sheetsandwich; 8 strands in 2 sheets; jelly-roll; similarity to the Nucleoplasmin-like/VPfoldβ-sheetsandwich; 8 strands in 2 sheets; jelly-rollβ-sheetsandwich; 8 strands in 2 sheets; jelly-rollβ-sheetsandwich; 8 strands in 2 sheets; greek-keyβ-sheetbeta-sandwich: 8 strands in 2 sheetsβ-sheetsandwich; 8 strands in 2 sheets; complex topology with the crossing loopsβ-sheetsandwich; 8 strands in 2 sheets; greek-key: partial topological similarity toimmunoglobulin-like foldsβ-sheetsandwich; 8 strands in 2 sheets; greek-key: partial topological similarity toimmunoglobulin-like foldsβ-sheetsandwich; 8 strands in 2 sheets; greek-key: partial topological similarity toimmunoglobulin-like foldsβ-sheetsandwich; 9 strands in 2 sheets; jelly-rollβ-sheetsandwich; 9 strands in 2 sheets; jelly-roll; form trimersβ-sheetsandwich; 9 strands in 2 sheets; greek-keyβ-sheetsandwich; 9 strands in 2 sheets; greek-keyβ-sheetsandwich; 9 strands in 2 sheets; greek-key/jelly-rollβ-sheetsandwich; 9 strands in 2 sheets; jelly-rollβ-sheetsandwich; 9 strands in 2 sheets; greek-key; contains a few helices in loop regionsβ-sheetsandwich; 9 strands in 2 sheets; unusual topology with 2 crossover loopsβ-sheetsandwich, 10 strands in 2 sheets; greek-keyβ-sheetsandwich, 10 strands in 2 sheets; jelly-rollβ-sheetsandwich, 10 strands in 2 sheets; jelly-rollβ-sheetsandwich, 10 strands in 2 sheets; “folded meander”β-sheetsandwich, 10 strands in 2 sheetsβ-sheetsandwich; 11 strands in 2 sheetsβ-sheetsandwich; 11 strands in 2 sheets; greek-keyβ-sheetsandwich; 11 strands in 2 sheets; greek-keyβ-sheetsandwich; 14 strands in 2 sheets; greek-keyβ-sheetsandwich; 12-14 strands in 2 sheets; complex topologyβ-sheetsandwich; 18 strands in 2 sheetsβ-sheetduplication: two beta-sandwiches of similar topologies are fused together in asingle three beta-sheet domainβ-sheetconsists of two beta-sandwich domains of similar topologiesβ-sheetconsists of two different beta-sandwich domains of partial topological similarityto immunoglobulin-like foldsβ-sheetconsists of two different beta-sandwich domains unrelated to other beta-sandwichfoldsβ-sheetconsists of two all-beta subdomains: conserved small domain has a rubredoxin-like fold; larger domain consists of 6 beta-stands packed in either sandwich oftwo 3-stranded sheets or closed barrel (n = 6; S = 8)β-sheetthis fold is formed by three glycine-rich regions inserted into a small 8-strandedbeta-sandwichβ-sheetbarrel, partly opened; n* = 4, S* = 8; meanderβ-sheetcontains barrel, partly opened; n* = 4, S* = 8; meanderβ-sheetcontains barrel, partly opened; n* = 4, S* = 8; meander; capped by alpha-helixβ-sheetcore: barrel, in some members open; n* = 4, S* = 8; meanderβ-sheetcore: barrel, open; n* = 4, S* = 8; meander; SH3-like topologyβ-sheetcore: barrel, open; n* = 4, S* = 8; meander; SH3-like topology; some similarity tothe Sm-like foldβ-sheetcore: barrel, open; n* = 4, S* = 8; meander; SH3-like topology; some similarity tothe Sm-like foldβ-sheetcore: barrel, closed; n = 4, S = 8; complex topology; helix-containing crossoverconnectionβ-sheetbarrel, closed; n = 5, S = 8, meanderβ-sheetbarrel, closed or partly opened n = 5, S = 10 or S = 8; greek-keyβ-sheetcore: barrel, partly opened; n* = 5, S* = 8; meanderβ-sheetbarrel, closed; n = 6, S = 12; and a hairpin triplet; meanderβ-sheetbarrel, closed; n = 6, S = 10; greek-keyβ-sheetbarrel, closed; n = 6, S = 10; greek-keyβ-sheetbarrel; n = 6, S = 10; greek-keyβ-sheetcore: barrel; n = 6, S = 10; greek-key; topologically similar to the FMN-binding splitbarrelβ-sheetsegment-swapped dimer forming two identical conjoint barrels (n = 6, S = 10)topologically similar to the FMN-binding split barrelβ-sheetbarrel, open; n* = 6, S* = 10; greek-keyβ-sheetbarrel, closed; n = 6, S = 8; greek-keyβ-sheetbarrel; n = 6, S = 8, greek-key; similar to one trypsin-like protease barrelβ-sheetbarrel; n = 6, S = 8, greek-keyβ-sheetbarrel, closed; n = 6, S = 8; greek-keyβ-sheetbarrel, closed; n = 6, S = 8, greek-key, partial similarity to the OB-foldβ-sheetbarrel, closed; n = 6, S = 10, complex topologyβ-sheetcore: barrel, closed; n = 6, S = 8; topology is similar to that of the acid proteasesbarrelβ-sheetbarrel, closed; n = 6, S = 8; a crossover loop topologyβ-sheetbarrel, closed; n = 6, S = 10; complex topology with crossover (psi) loopsβ-sheetbarrel, closed; n = 6, S = 10; complex topologyβ-sheetbarrel, closed; n = 6, S = 10; meander; capped at both ends by alpha-helicesβ-sheetbarrel, partly opened; n* = 6, S* = 12; meander; capped by an alpha-helixβ-sheetbarrel, closed; n = 6, S = 12; mixed beta-sheetβ-sheetcore: barrel, closed; n = 7, S = 8; complex topologyβ-sheetbarrel, closed; n = 7, S = 10; complex topologyβ-sheetbarrel, closed; n = 7, S = 10; order: 1234765; strands 1 and 5 are parallel to eachotherβ-sheetbarrel, closed; n = 7, S = 10; complex topologyβ-sheetbarrel, closed; n = 7, S = 10; greek-key topology; one overside connectionβ-sheetbarrel, closed; n = 7, S = 10; complex topologyβ-sheetcore: barrel, closed; n = 7, S = 12; meanderβ-sheetbarrel, closed or opened; n = 8, S = 12; meanderβ-sheetbarrel, closed; n = 8, S = 10; meanderβ-sheetbarrel, closed; n = 8, S = 10; complex topologyβ-sheetbarrel, closed; n = 8, S = 10; one overside connectionβ-sheetbarrel, closed; n = 8, S = 10; mixed sheet; two overside connectionsβ-sheetbarrel, partly open; n* = 8, S* = 10; one psi loopβ-sheetdimer of two non-identical subunits; forms two similar barrels, n = 8, S = 10 each,that are fused together with the formation of third barrel, n = 6, S = 8β-sheetconsists of four 4-stranded beta-sheet motifs; meanderβ-sheetconsists of five 4-stranded beta-sheet motifs; meanderβ-sheetconsists of six 4-stranded beta-sheet motifs; meanderβ-sheetconsists of seven 4-stranded beta-sheet motifs; meanderβ-sheetconsists of eight 4-stranded beta-sheet motifs; meanderβ-sheetfolded sheet; greek-keyβ-sheetcore: 3-stranded meander beta-sheetβ-sheetsmall mixed beta-sheet, 4 “generalized” strandsβ-sheetcoiled antiparallel beta-sheet of 5 strands, order 51324; complex topology,crossing loopsβ-sheettwisted meander beta-sheet of 6 strandsβ-sheetcore: twisted 7-stranded beta-sheet (half-barrel) of complex topologyβ-sheetcore: twisted 7-stranded beta-sheet (half-barrel)β-sheetsingle sheet; 10 strandsβ-sheet11 stranded sheet partly folded in a corner-like structure filled with a few shorthelicesβ-sheetsingle sheet; 16 strands; meanderβ-sheetsingle sheet formed by beta-hairpin repeats; exposed on both sides in the middleβ-sheetconsists of 3 4-stranded sheets; strands are parallel to the 3-fold axisβ-sheetconsists of 3 4-stranded sheets; strands are perpendicular to the 3-fold axisβ-sheetsuperhelix turns are made of parallel beta-strands and (short) turnsβ-sheetsuperhelix turns are made of parallel beta-strands and (short) turnsβ-sheetone turn of helix is made by two pairs of antiparallel strands linked with shortturnsβ-sheet(homo)trimer; each chain donates 3 beta-strands per turn of the helixβ-sheettrimer formed by the interlocking beta-hairpin repeat unitsβ-sheettrimer; contains two different beta-prism-like domains connected by an linkersubdomain of less regular structureβ-sheetTrp-rich beta-hairpin repeat units form helical structures of 3 units per turnβ-sheetsandwich of half-barrel shaped beta-sheetsβ-sheetdouble-stranded ribbon sharply bent in two places; the ribbon ends formincomplete barrel; jelly-rollβ-sheetmultisheet protein with a mixture of beta-sandwich and beta-prism featuresβ-sheetmultisheet protein containing partial beta-propeller and beta-sandwich regionsβ-sheetmultisheet protein with a mixture of beta-sandwich and beta-barrel featuresβ-sheetcomplex fold made of five beta-hairpin units and a b-ribbon arcβ-sheetcomplex fold made of several coiled beta-sheets; contains an SH3-like barrelβ-sheetcomplex fold made of several coiled beta-sheetsβ-sheetcomplex fold made of several coiled beta-sheetsβ-sheetcomplex foldβ-sheetcomplex fold; consists of two intertwined subdomainsβ-sheetcomplex foldβ-sheetcomplex fold made of bifurcated and partly folded beta-sheetβ-sheetcomplex fold made of bifurcated and coiled beta-sheetsβ-sheetcomplex fold made of bifurcated and coiled b-sheetsβ-sheetpseudobarrel; mixed sheet of 7 strand folded upon itself and “buckled” by twobeta-turnsβ-sheetpseudobarrel; sandwich of two sheets packed at a positive interstrand angle andinterconnected with many short turnsβ-sheetpseudobarrel; capped on both ends by alpha-helicesβ-sheetpseudobarrel; capped at one end by an alpha-helixβ-sheetpseudobarrel; capped on both ends by alpha-helicesβ-sheetpseudobarrel; mixed folded sheet of 5 strands; order 13452; strand 1 and 3 areparallel to each otherβ-sheetpseudobarrel; some similarity to OB-foldβ-sheetnon-globular proline-rich hairpinα/βcontains parallel beta-sheet barrel, closed; n = 8, S = 8; strand order 12345678α/βcore: 3 layers, a/b/a; parallel beta-sheet of 6 strands, order 321456α/βcore: 3 layers, b/b/a; central parallel beta-sheet of 5 strands, order 32145; topantiparallel beta-sheet of 3 strands, meanderα/β3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-likeα/β3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; incompleteRossmann-like fold; binds UDP groupα/βvariant of beta/alpha barrel; parallel beta-sheet barrel, closed, n = 7, S = 8; strandorder 1234567; some members may have fewer strandsα/βcontains: barrel, closed; n = 10, S = 10; accommodates a hairpin loop inside thebarrelα/β3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; thereare some variations in topologyα/β2 layers, a/b; parallel beta-sheet of 3 strands, order 123α/βcore: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1234; structuralsimilarity of the MurF and HprK extends beyond the core.α/β2 curved layers, a/b; parallel beta-sheet; order 1234...N; there are sequencesimilarities between different superfamiliesα/βcore: three turns of irregular (beta-beta-alpha)n superhelixα/βcore: 4 turns of a (beta-alpha)n superhelixα/βcore: 4 turns of (beta-beta-alpha)n superhelixα/β3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134α/β3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134α/β3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134α/β3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134α/β3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134α/β3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134α/βcore: 3 layers: a/b/a; parallel beta-sheet of 4 strands; 2134α/β3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134α/β3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134α/β3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 3214α/β3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 1423α/β3 layers, a/b/a; parallel beta-sheet of 5 strands, order 21345α/β3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145α/β3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145α/βcore: 3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145α/β3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-likeα/β3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-likeα/β3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 43215α/β3 layers, a/b/a; core: parallel beta-sheet of 5 strands, order 32145α/β3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 21354; topologicalsimilarity to a part of the arginase/deacetylase foldα/βcore: 3 layers: a/b/a, parallel beta-sheet of 5 strands, order 21435; contains a deeptrefoil knotα/β3 layers: a/b/a; parallel or mixed beta-sheet of 4 to 6 strandsα/β3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; Rossmann-likeα/β3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456α/β3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456α/β3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; also contains a C-terminal alpha + beta subdomainα/β3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456α/β3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456α/βcore: 3 layers: a/b/a; parallel or mixed beta-sheet of 6 strands, order 321456α/β3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456α/β3 layers: a/b/a; parallel beta-sheet of 6 strands, order 432156α/β3 layers: a/b/a; parallel beta-sheet of 6 strands, order 342156α/β3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213456α/β3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213465α/β3 layers: a/b/a, parallel or mixed beta-sheets of variable sizesα/β3 layers: a/b/a, parallel beta-sheet of 6 strands, order 324156α/β3 layers, a/b/a; parallel beta-sheet of 7 strands, order 7165243α/β3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567α/β3 layers: a/b/a, parallel beta-sheet of 7 strands, order 4321567α/β3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3421567α/β3 layers: a/b/a, parallel beta-sheet of 7 strands, order 2314567; left-handedcrossover connection between strands 2 & 3α/βcore: 3 layers, a/b/a; parallel beta-sheet of 7 strands, order 2134756α/β3 layers: a/b/a, parallel beta-sheet of 8 strands, order 21387456α/β3 layers: a/b/a; parallel beta-sheet of 8 strands, order 54321678α/βbeta(2)-(alpha-beta)2-beta; 2 layers, a/b; mixed beta-sheet of 5 strands, order12345; strands 1 & 5 are antiparallel to the restα/βbeta(2)-(alpha-beta)2-beta(3); 3 layers, a/b/b; some topological similarity to theN-terminal domain of MinCα/βcore: 2 layers, a/b; mixed beta-sheet of 6 strands, order 324561; strands 3 & 6 areantiparallel to the restα/β3 layers: a/b/a; parallel beta-sheet of 4 strands, order 2134α/βcore: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1423α/β3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451α/βcore: 3 layers, a/b/a; mixed beta-sheet of 4 strands, order 4312; strand 3 isantiparallel to the restα/β3 layers: a/b/a; mixed beta-sheet of 4 strands, order 2143, strand 4 is antiparallelto the restα/β3 layers: a/b/a; mixed beta-sheet of 5 strands, order 13245, strand 1 is antiparallelto the restα/β3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145, strand 5 is antiparallelto the restα/β3 layers: a/b/a; mixed beta-sheet of five strands, order 21345; strand 4 isantiparallel to the restα/βcore: 3 layers, b + a/b/a; the central mixed sheet of 5 strands: order 21534; strand2 is antiparallel to the restα/βcore: 3 layers, a/b/a; mixed beta-sheet of 5 strands, order 12345; strands 2 &, insome families, 5 are antiparallel to the restα/βCore: 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 isantiparallel to the restα/β3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallelto the restα/β3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallelto the restα/βcore: 3 layers, a/b/a; mixed sheet of 5 strands: order 21354; strand 4 isantiparallel to the rest; contains crossover loopsα/β3 layers: a/b/a; mixed beta-sheet of 5 strands; order: 21354, strand 5 is antiparallelto the rest; permutation of the Phosphorylase/hydrolase-like foldα/β3 layers: a/b/a; mixed beta-sheet of five strands, order 21345; strand 1 isantiparallel to the restα/β3 layers: a/b/a; mixed beta-sheet of 6 strands; order: 213546, strand 5 isantiparallel to the rest; topological similarity to the MogA-like family foldα/β3 layers, a/b/a; core: mixed beta-sheet of 6 strands, order 213456, strand 6 isantiparallel to the restα/β3 layers: a/b/a; mixed beta-sheet of 6 strands, order 165243, strand 3 isantiparallel to the restα/β3 layers: a/b/a; mixed beta-sheet of 6 strands, order 126345; strand 1 isantiparallel to the restα/βcore: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 324156; strand 5 isantiparallel to the restα/βcore: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 isantiparallel to the restα/βcore: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 isantiparallel to the restα/β3 layers: a/b/a; mixed beta-sheet of 6 strands, order 231456; strand 3 isantiparallel to the restα/β3 layers: a/b/a; mixed beta-sheet of 6 strands, order 251634; strand 6 isantiparallel to the restα/βcore: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 432156; strand 4 isantiparallel to the restα/βcore: 3 layers, a/b/a; mixed sheet of 7 strands, order 1237456; strands 1, 6 and 7are antiparallel to the restα/β3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 isantiparallel to the restα/βcore: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 isantiparallel to the restα/β3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 isantiparallel to the rest; topological similarity to SAM-dependentmethyltransferasesα/βmain domain: 3 layers: a/b/a, mixed beta-sheet of 7 strands, order 3245671; strand7 is antiparallel to the restα/β3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214657; strand 6 isantiparallel to the restα/β3 layers: a/b/a; mixed beta-sheet of 8 strands, order 32145678; strands 6 and 8 areantiparallel to the restα/βcore: 3 layers, a/b/a; mixed beta-sheet of 8 strands, order 12435678, strand 2 isantiparallel to the restα/βcore: 3 layers, a/b/a; mixed beta-sheet of 8 strands, order 32145687; strand 7 isantiparallel to the restα/β3 layers: a/b/a; mixed beta-sheet of 8 strands, order 34251687; strand 8 isantiparallel to the restα/βcore: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 isantiparallel to the restα/β3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 32145678;strand 8 is antiparallel to the restα/β3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 34215786;strand 8 is antiparallel to the restα/βcore: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 45321678, strands 4 and5 are antiparallel to the restα/βcore: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 43516728, strand 7 isantiparallel to the restα/β3 layers: a/b/a; mixed beta-sheet of 8 strands, order 78612354; strands 3, 4 and 8are antiparallel to the restα/β3 layers: a/b/a; mixed beta-sheet of 9 strands, order 918736452; strands 1, 2 and 8are antiparallel to the restα/β3 layers: a/b/a; mixed (mostly antiparallel) beta-sheet of 9 strands, order432159876; left-handed crossover between strands 4 and 5α/β3 layers: a/b/a; mixed beta-sheet of 9 strands, order 342156798; strands 3, 8 and 9are antiparallel to the rest; left-handed crossover connection between strands 6and 7α/βconsists of two intertwined (sub)domains related by pseudo dyad; duplicationα/βpossible duplication: the topologies of N- and C-terminal halves are similar; 3layers: a/b/a; single mixed beta-sheet of 10 strands, order 213549A867 (A = 10);strands from 5 to 9 are antiparallel to the restα/βconsists of two similar domains related by pseudo dyad; duplicationα/βconsists of two similar domains related by pseudo dyad; duplicationα/β3 layers: a/b/a; parallel beta-sheet of 5 strands, order 21345α/βcontains of two similar intertwined domains related by pseudo dyad; duplicationα/βconsists of two similar domains with 3 layers (a/b/a) each; duplicationα/βconsists of three similar domains with 3 layers (a/b/a) each; duplicationα/βconsists of three similar domains with 3 layers (a/b/a) each; duplicationα/βconsists of two domains of similar topology, 3 layers (a/b/a) eachα/βconsists of two non-similar domains, 3 layers (a/b/a) eachα/βconsists of two non-similar domains with 3 layers (a/b/a) eachα/βconsists of two non-similar alpha/beta domains, 3 layers (a/b/a) eachα/βconsists of two non-similar domains, 3 layers (a/b/a) eachα/βconsists of two non-similar domainsα/βconsists of two non-similar domainsα/β2 different domains; d1: [core: 3 layers, a/b/a; parallel sheet of 5 strands, order:2134]; D2: [2 layers, a/b; mixed sheet of 6 strands, order 321645; strands 2 and 6are antiparallel to the rest]α/βconsists of two non-similar domainsα/βconsists of two different alpha/beta domains; (1) of the Flavodoxin-like fold(scop_cf 52171); (2) similar to the Restriction endonuclease-like fold (scop_cf52979), inserted into domain 1α/βcontains a P-loop NTP-binding motif; mixed beta-sheet folds into a barrel-likestructure with helices packed on one sideα/βcontains mixed beta-sheets; topology is partly similar to that of the catalytic C-terminal domainα/βduplication: tandem repeat of two domains; 3 layers (a/b/a); parallel beta-sheet of4 strands, order 2134α/βconsists of two similar intertwined domain with 3 layers (a/b/a) each: duplicationα/βconsists of two similar intertwined domain with 3 layers (a/b/a) each: duplicationα/βconsists of two similar domains related by pseudo dyad; duplicationα/βconsist of two intertwined domains; duplication: contains two structural repeats ofalpha-beta-(beta-alpha)3 motif with mixed beta-sheet, order: 1432, strand 1 isantiparallel to the restα/βconsist of two intertwined domains; contains partial duplicationα/βconsist of two different alpha/beta domains; N-terminal domain has a SurE-liketopology with a left-handed beta-alpha-beta unitα/βcore: alpha-beta(2)-(alpha-beta)2; 3 layers (a/b/a); mixed beta-sheet of 4 strands,order 2134; strand 2 is antiparallel to the restα/βsingle helix packs against antiparallel beta-sheetα/βcommon alpha + beta motif for the active site regionα/βconsists of one alpha-helix and 4 strands of antiparallel beta-sheet and containsthe catalytic triad Cys-His-Asnα/βcore: (alpha)-beta-omega_loop-beta-alpha; embeded in larger different structuresα/βcontains long curved beta-sheet and 3 helicesα/βbeta-alpha-beta-alpha(2); antiparallel beta-ribbonα/βbeta-alpha(2)-beta; antiparallel strandsα/βalpha-beta(2)-alpha; antiparallel hairpinα/βalpha-beta(2)-alpha; 2 layers a/b; antiparallel beta-hairpinα/βalpha(3)-beta(2); antiparallel hairpinα/βbeta(3)-alphaα/βbeta(3)-alpha; 2 layers: alpha/betaα/βalpha1-beta3; 2 layers: alpha/beta; order 132α/βbeta-alpha-beta(2); 2 layers: alpha/beta; antiparallel beta-sheet: order 132α/βbeta-(alpha)-beta-alpha-beta(2); 3 layers: alpha/beta/alpha; antiparallel beta-sheet:order 1243α/βbeta-(2)-alpha(2)-beta(2); 2 layers: beta/alpha; antiparallel beta-sheet: order 1243;topological similarity to the common core of ribosomal proteins L23 and L15eα/βbeta-(2)-alpha(3)-beta(2); 2 layers: beta/alpha; mixed beta-sheet: order 1234;stands 2 and 3 a parallel to each otherα/βalpha-beta(3)-alpha-beta(2); 3 layers: alpha/beta/alphaα/βalpha-beta(3)-alpha-beta(2)-alpha; 2 layers: alpha/betaα/βbeta(2)-alpha(2)-beta; 2 layers: 3-stranded antiparallel beta-sheet, order 213; HTHmotif; also includes the extra N-terminal, DNA minor groove-binding helixα/βalpha-beta(4)-alpha-beta(2)-alpha; 2 layers: alpha/betaα/βbeta(4)-alpha-beta(2)-alpha; 2 layers: alpha/beta; antiparallel beta-sheet, order:651234α/βcore: beta(3)-alpha-beta-alpha; 2 layers: alpha/beta; left-handed crossoverα/βcore: beta(2)-alpha-beta(2); mixed beta-sheet 2143α/βalpha + beta sandwichα/βCore: alpha-beta(4); helix packs against coiled antiparallel beta-sheetα/βalpha-beta-alpha-beta-alpha(2)-beta(3); antiparallel beta-sheet; order: 15432α/βalpha(2)-beta(4)-alpha, 2 layers: alpha/beta, antiparallel beta sheet, meanderα/βbeta(3)-alpha-beta(2)-alpha; 2 layers, alpha/beta; antiparallel beta-sheet, order:12543α/βcore: alpha-beta(3)-alpha, 2 layers: alpha/beta, three-stranded antiparallel betasheet, strand order 123α/βcore: beta(2)-alpha(2), 2 layers: alpha/beta; long C-terminal helix forms dimericparallel and tetrameric antiparallel coiled coilsα/βhelix-swapped dimer of beta(4)-alpha motifsα/βbeta-BETA(2)-beta-alpha-beta(2); antiparallel sheet: order 2134 packed againsthelix and BETA-hairpin on the same side; irregular C-terminal tailα/βDimericα/βalpha-beta(4)-alpha(3); core: meander beta-sheet plus one helix 2α/βcore: three short helices packed against a barrel-like beta-sheet; some similarity tothe SH3-like foldα/βbeta*-alpha-beta(2)-alpha-beta-alpha; mixed beta sheet forms a partly openbarrel: (n* = 4, S* = 8)α/βbeta-alpha-beta(4)-alpha-beta(2); contains beta-sheet barrel (n = 5, S = 8)α/βbeta(3)-alpha(2)-beta; 2 layers; mixed beta-sheet, order 4123, strands 1 and 4 areparallel to each otherα/βmixed beta-sheet folds into a barrel (n = 8, S = 14) around the central helixα/βbeta-sheet folds into a barrel (n = 11, S = 14) around the central helixα/βbeta-sheet folds into a barrel (n = 12, S = 12) around the central helixα/βcontains very long N-terminal helix, which end is packed against beta-sheetα/βcore: beta(7)-alpha(2); N- and C-terminal extensions form a coiled coilsubdomainα/βbeta(6)-alpha; antiparallel beta-sheet, meanderα/βbeta(3)-alpha-beta(3)-alpha; 3 layers a/b/aα/βalpha(2)-beta(5)-alpha(2); 3 layers a/b/a; meander beta-sheetα/βcore: beta(2)-alpha-beta(2); antiparallel beta-sheetα/βbeta(4)-alpha-beta; 2 layers: alpha/beta; mixed beta-sheet, order: 51234α/βalpha-beta-X-beta(2); 2 layers: alpha/beta; mixed beta-sheet, order: 123α/βbeta-alpha-beta-(alpha)-beta(2); 2 layers: alpha/beta; mixed beta-sheet, order:1342α/βbeta(2)-alpha-beta; 2 layers: alpha/betaα/βbeta-alpha-beta(3); 2 layers: alpha/betaα/βbeta-alpha-beta(3); 2 layers: alpha/betaα/βbeta(2)-alpha-beta(3); 2 layers: alpha/betaα/βmultiple repeats of beta(2)-alpha(2) motifα/βbeta(2)-alpha(3)-beta; two layers: alpha/beta; antiparallel sheet: order 213α/βbeta(4)-alpha(2); two layers: alpha/beta; antiparallel sheet: order 1432α/βbeta(2)-alpha(2)-beta(2)-alpha-beta; two layers: alpha/beta; antiparallel sheet:order 51234α/βbeta-alpha(2)-beta(4)-alpha-beta(2); two layers: alpha/beta; bifurcated coiledbeta-sheet: order of the first 5 strands: 23154α/βbeta(4)-alpha(2)-beta(2)-alpha; antiparallel sheet: order 123465α/βbeta-alpha-beta(6)-alpha(2); antiparallel sheet: order 165432α/βbeta(3)-alpha(2)-beta-alpha(2)-beta3; 2 layers alpha/beta; antiparallel sheet: order1234567α/βalpha-beta(6)-alpha(2)-beta-alpha(n); 3 layers alpha/beta/alpha; antiparallel sheet:order 1234567α/βbeta(4)-alpha-beta(2)-alpha(2); mixed, predominately antiparallel beta-sheet,order: 123465, strands 4 and 5 are parallel to each otherα/βcore: beta-alpha-beta(4); 2 layers: alpha/betaα/βcore: beta-alpha-beta(4); 2 layers: alpha/betaα/βcore: beta-alpha(2)-beta-X-beta(2); 2 layers: alpha/beta; antiparallel beta-sheet:order 1342α/βalpha + beta sandwich; loop across free side of beta-sheetα/βalpha-beta-loop-beta(3); loop across free side of beta-sheetα/βcore: beta-BETA-alpha-beta-BETA-beta-alpha; contains a beta-hammerheadmotif similar to that in barrel-sandwich hybridsα/βcore: beta(2)-alpha(2)-beta(2)-alpha(2); 2 layers a/b; mixed sheet: 2143α/βbeta(2)-alpha(n)-beta: 2 layers a/b; antiparallel sheet: 123α/βalpha-beta(2)-alpha-beta-alpha(2); 3 strands of antiparallel sheet: 213α/βbeta-alpha(2)-beta-alpha-beta; 2 layers, alpha/betaα/βbeta-alpha-beta(2)-alpha(2); 3 layers, alpha/beta/alpha; antiparallel beta-sheet:order 123α/βbeta-alpha(2)-beta(2); 2 layers, alpha/beta; antiparallel beta-sheet: order 123α/βalpha-beta(3)-alpha(2); 2 layers, alpha/betaα/β(beta)-alpha-beta(3)-alpha; 2 layers, alpha/betaα/βalpha-beta(3)-alpha; 2 layers: alpha/betaα/βduplication: consists of two beta(3)-alpha repeats; 3 layers, beta/alpha/betaα/βbeta-alpha-beta(2)-alpha; 2 layers: alpha/betaα/βalpha(2)-beta(3)-alpha(3); 2 layers alpha/beta, 3-stranded antiparallel beta-sheet;order 123α/βalpha(3)-beta-alpha(2)-beta(2); 2 layers alpha/beta, 3-stranded antiparallel beta-sheet; order 123α/βbeta-alpha(2)-beta(2)-alpha; 2 layers: alpha/betaα/βcore: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/betaα/βcore: alpha-beta-turn-beta-X-beta-(alpha); mixed beta-sheet, order of core strands:123α/βalpha(2)-beta(4); 2 layers: alpha/beta; antiparallel beta-sheet: order 2143α/βalpha-beta(3)-alpha-beta-alpha; bifurcated coiled beta-sheetα/βbeta(3)-alpha(3); meander and up-and-down bundleα/βbeta-alpha(3)-beta(2); 2 layers: alpha/beta; related to the enolase/MLE N-domainfold by a circular permutationα/βalpha-beta-alpha(3)-beta(2); 2 layers: alpha/beta;α/β3-helical bundle packed against 3-stranded mixed beta-sheetα/βbeta(3)-alpha(4); meander beta-sheet packed against array of helices; containsPro-rich stretchα/βbeta(3)-alpha(5); meander beta-sheet packed against array of helicesα/βbeta-alpha-beta(2)-alpha; 2 layers: alpha/beta; mixed sheet 213; crossing loopsα/βalpha-beta(3)-alpha(3); 2 layers, a/b; mixed beta-sheet, order: 132; crossing loopsα/βalpha + beta sandwich with antiparallel beta-sheet; (beta-alpha-beta) × 2α/βconsists of two alpha + beta subdomains with some similarity to the ferredoxin-likefoldα/βbeta-alpha-beta-X-beta(2)-alpha(2)-beta; antiparallel beta-sheet, order 24153;topological similarity to the ferredoxin-like fold (scop_cf 54861)multicontains a cluster of helices and a beta-sandwichmulticontains a cluster of helices and a beta-sandwichmulticontains a cluster of helices and an alpha + beta sandwichmulticonsists of an all-alpha and alpha + beta domainsmulticontains a helical bundle with a buried helix and an alpha + beta insert domainmulticonsists of an all-alpha and alpha + beta domains connected by antiparallel coiledcoilmulticontains a cluster of helices and an alpha/beta domainmulticontains an (8,10) beta-barrel and an all-alpha domainmulti2 domains: (1) all-alpha: 5 helices; (2) contains an open beta-sheet barrel: n* = 5,S* = 8; complex topologymultiN-terminal domain is an alpha + beta, C-terminal domain is an alpha/beta withmixed beta-sheetmultidivided into morphological domains including “palm”, “thumb” and “fingers”; thecatalytic “palm” domain is conserved to all membersmultiMultidomain subunits of complex domain organizationmulti3 domains: (1&2) alpha + beta, with domain 2 being inserted in domain 1; (3) all-alphamulti4 domains: (1) Toprim alpha/beta; (2&4) “winged helix”-like; (3) barrel: n = 6,S = 8multi4 domains: (1) toprim alpha/beta; (2) “winged helix”-like; (3) alpha + beta; (4) all-alphamulti2 domains: (1) toprim alpha/beta; (2) “winged helix”-likemulti2 domains: (1) alpha + beta; (2) toprim alpha/betamulticonsists of three domains: alpha-helical dimerisation domain (res. 1-53) withHhH motif (Pfam 00633); ‘treble cleft’ C4 zinc-finger domain (54-76; Pfam02132); and Toprim domain (76-199; segment-swapped dimer; Pfam 01751)multi2 domains: alpha + beta and all-betamulti2 domains: (1) alpha + beta: beta3-alpha2-beta2; (2) alpha/beta, a part of its mixedsheet forms barrel: n = 6, S = 8multi3 domains: (1) all-alpha; (2&3) alpha + betamulti2 domains: (1) alpa/beta; (2) Fe—S cluster-boundmulti2 domains: (1) alpha/beta of a Rossmann-fold topology, binds NAD (2)multihelical arraymulti4 domains: (1&2) duplication: share the same alpha/beta fold; (3) beta-barrel; (4)alpha + betamulti2 domains: (1) alpha + beta; (2) alpha/beta (interrupts domain 1)multi4 domains: (1) 3-helical bundle; (2) alpha + beta of ferredoxin-like fold (3 and 4)alpha + beta of dsRDB-like foldmulti3 domains: (1) 3-helical bundle; (2 and 3) alpha + beta of different folds: domain 3has a ferredoxin-like fold and is inserted in domain 2multi3 domains: (1) 4-helical bundle; (2) alpha + beta; (3) “winged helix”-likemulti3 domains: (1 and 2) alpha + beta; (3) mostly alpha, inserted in domain 2multi3 domains: (1) spectrin repeat-like 3-helical bundle; (2 and 3) alpha/beta:Rossmann-fold topologymulti3 domains: (1) protozoan pheromone-like alpha-helical bundle; (2) rubredoxin-like domain lacking metal-binding site; (3) alpha + beta heterodimerisationdomain: alpha-beta(5)-alphamulti2 domains: (1) alpha-helical bundle; (2) beta-barrel (n = 5, S = 8)multi3 domains: (1) alpha-helical bundle; (2&3) complex all-beta foldsmulti2 closely associated domains: (1) all-alpha, EF-hand like; (2) alpha + beta,Frataxin-likemulti2 domains; d1: [all-alpha; 3-helical bundle, similar to theimmunoglobulin/albumin-binding domain-like fold (scop_cf 46996)]; d2:[alpha/beta; 3 layers, a/b/a; 6-stranded mixed beta-sheet, order: 321456, strand 6is antiparallel to the rest]multi3 domains; d1: alpha + beta [alpha(2)-beta(3); mixed sheet: 213]; d2: alpha/beta ofthe NAD(P)-binding Rossmann-fold superfamily (scop_sf 51735, most similar toscop_fa 51883 and scop_fa 51736); d3: alpha + beta of the glutaminesynthetase/guanido kinase fold (scop_cf 55930); d1 and d3 form a single beta-sheetmulti2 domains: d1 [alpha/beta; related to the PFK N-terminal domain (scop_sf53784)]; d2 [all-beta; atypical beta-sandwich made of 4 structural repeats ofbeta(3) unit]multi2 domains; d1 (1-64, 174-335) [alpha/beta; 3 layers, a/b/a; mixed beta sheet of 9strands, order: 219863457; strands 1, 5 and 8 are antiparallel to the rest]; d2 (65-142)[all-beta; barrel, closed (n = 6, S = 10); greek-key; topologically similar to thesplit barrel fold (scop_cf 50474)multi2 domains; (1) alpha + beta (res 1-192), a circularly permuted rS5 domain 2-likefold (scop_cf 54210); (2) alpha/beta with parallel beta-sheet of 4 strands, order2134multiconsists of two domains; d1: alpha + beta (78-190; alpha-beta(4)-alpha-beta-alpha;3 layers; antiparallel beta-sheetof 5 strands; order 51234); d2: alpha/beta similarto the G-domain fold (191-381; scop_fa 52592)multi2 domains: (1) all-alpha, (2) alpha + beta; asymmetric homodimer with eachdomain intertwining with its counterpartmulti4 domains: three intertwined predominately alpha domains and one jelly-roll beta-sandwichmultilarge protein without apparent domain division; has a number of all-alpha regionsand one all beta domain near the C-endmultilarge protein without apparent domain divisionmultilarge protein without apparent domain divisionmembrane +multi-helical domains of various folds which unfold in the membranesurfacemembrane +core: up-and-down bundle of seven transmembrane helices tilted 20 degrees withsurfacerespect to the plane of the membranemembrane +five transmembrane helices forming a sheet-like structuresurfacemembrane +12 transmembrane helices in an approximate threefold rotational symmetricsurfacearrangementmembrane +core: 7 transmembrane helices organized into two bundles, one formed by thesurfacefirst two helices and the other by the restmembrane +two antiparallel transmembrane helicessurfacemembrane +core: up-and-down bundle of four transmembrane helicessurfacemembrane +core: 8 helices, 2 short helices are surrounded by 6 long transmembrane helicessurfacemembrane +11 transmembrane helices; duplication: consist of 2 structural repeats of fivesurfacehelices each plus extra C-terminal helixmembrane +12 transmembrane helices; duplication: the N- and C-terminal halves aresurfacestructurally similarmembrane +core: 18 transmembrane helicessurfacemembrane +oligomeric transmembrane alpha-helical proteinssurfacemembrane +oligomeric transmembrane alpha-helical proteinsurfacemembrane +oligomeric transmembrane alpha-helical proteinsurfacemembrane +heteropentameric transmembrane alpha-helical protein; 4 transmembrane helicessurfaceper subunitmembrane +oligomeric fold; 3 transmembrane helices per subunitsurfacemembrane +oligomeric fold; 3 transmembrane helices per subunitsurfacemembrane +9 transmembrane helicessurfacemembrane +10 transmembrane helices forming of a gated channelsurfacemembrane +core: 11 transmembrane helicessurfacemembrane +core: hairpin of two transmembrane helicessurfacemembrane +core: three transmembrane helices, bundlesurfacemembrane +multihelical; complex architecture with several transmembrane helicessurfacemembrane +multihelical; complex architecture with several transmembrane helicessurfacemembrane +12 transmembrane helices; duplication: the N- and C-terminal halves of the wholesurfaceproteins are structurally similarmembrane +core: three transmembrane helices, up-and-down bundlesurfacemembrane +core: four transmembrane helices, up-and-down bundle, binds one or two hemesurfacegroups in between the helicesmembrane +membrane-associated alpha-helical protein; no transmembrane helicessurfacemembrane +membrane-associated alpha-helical protein; no transmembrane helicessurfacemembrane +2 helices, hairpinsurfacemembrane +core: multihelical; consists of three transmembrane regions of 2, 2 and 6 helices,surfaceseparated by cytoplasmic domainsmembrane +membrane all-alpha foldsurfacemembrane +membrane all-alpha fold; 6-helical “barrel” with internal binding cavitysurfacemembrane +membrane all-alpha fold; three transmembrane helicessurfacemembrane +, gathers together transmembrane barrels of different (n, S)surfacemembrane +subunit fold contains tandem repeat of alpha-beta hairpin-alpha(2) motifsurfacemembrane +consists of three domains: beta-barrel (res. 29-38, 170-259; scop_cf 50412);surfacebarrel-sandwich hybrid (39-72, 135-169; scop_sf 51230) and long alpha-hairpin(73-134; scop_cf 46556)membrane +subunit fold contains beta-sandwich of Ig-like (grerk-key) topology and a beta-surfaceribbon arm that forms an oligomeric transmembrane barrelmembrane +contains several large open beta-sheetssurfacemembrane +3 domains: (1) alpha + beta; (2&3) all-betasurfacemembrane +2 domains: (1) alpha + beta; (2) all-beta, similar to the CalB domain fold but thesurfacetwo last strands are transposedmembrane +2 intertwined domains; all-beta and alpha + betasurfacemembrane +2 domains; d1: complexed all-beta fold; d2: coiled-coil (trimeric) helical regionsurfacemembrane +3 intertwined all-beta domainssurfacemembrane +trimer; one subunit consists of an alpha/beta oligomerization subdomain [3-surfacestranded parallel beta-sheet, order 213], and an antiparallel coiled coilmembrane +4 domains; I (res. 14-225) and II (226-487) are beta-sandwiches of similarsurfacegamma-crystallin like topologies; III (488-594) has a beta-grasp like fold; IV(595-735) has an Ig-like foldOthernearly all-alphaOtherdisulfide crosslinked alpha-helical hairpinOtherdisulfide-bound fold; contains beta-hairpin with two adjacent disulfidesOtherdisulfide-rich fold; all-beta: 3 antiparallel strandsOtherdisulfide-rich fold; all-beta: 3 antiparallel strandsOtherdisulfide-rich fold; all-beta: 3 antiparallel strandsOtherdisulfide-rich; alpha + beta: 3 antiparallel strands followed by a short alpha helixOtherdisulfide-rich fold: nearly all-betaOtherdisulfide-rich alpha + beta foldOtherDisulfide-rich fold, nearly all-betaOtheralpha + beta fold with two crossing loopsOtherdisulfide-rich foldOtherdisulfide-rich calcium-binding foldOtherdisulfide-rich alpha + beta foldOtherdisulfide-rich fold; nearly all-betaOtherdisulfide-rich small alpha + beta fold; topological similarity to the Ovomucoiddomain IIIOtherdisulfide-rich fold; common core is alpha + beta with two conserved disulfidesOtherdisulfide-rich fold; all-beta; duplication: contains two structural repeatsOtherdisulfide-rich fold; common core is all-betaOtherdisulfide-rich all-beta foldOtherdisulfide-rich all-alpha foldOthersmall disulfide-richOtherdisulfide-rich; nearly all-betaOtherdisulfide-rich; nearly all-betaOtherdisulfide-rich; alpha + betaOtherduplication: consists of three similar disulfide-rich domainsOtherduplication: consists of two similar disulfide-rich domains, alpha + betaOtherdisulfide-rich; all-beta: open barrel, 5 strands; OB-fold-likeOtherdisulfide-rich, all-betaOtherdisulfide-rich, alpha + betaOtherdisulfide-rich, alpha + betaOtherdisulfide-rich, alpha + betaOtherdisulfide-rich, alpha + betaOtherdisulfide-richOtherdisulfide-rich, all-alphaOtherdisulfide-rich; all-alphaOtherdisulfide-rich, alpha + betaOtherdisulfide-richOtherdisulfide-rich; all-alpha; calcium-bindingOtherdisulfide-richOtherdisulfide-rich all-beta fold; contains beta sandwich of 5 strandsOtherdisulfide-rich six-stranded beta-sandwich; jelly-rollOtherbipartite cysteine-rich all-alpha domain; a single helix in the N-terminal part(chain A) is linked by disulfides to the C-terminal part (chain B) [3-helical bundleof the RuvA C-terminal domain-like fold (scop_cf 46928)OtherCalcium ion-boundOthera few helical turns and a disulfide-crosslinked loopOthera few helical turns assembled without a hydrophobic core?Otherfolds around 4Fe—4S clusterOtherfolds around 4Fe—4S clusterOtheralpha + beta metal(zinc)-bound fold: beta-hairpin + alpha-helixOtherall-alpha dimetal(zinc)-bound foldOtheralpha + beta metal(zinc)-bound foldOtherconsist of two different zn-binding subdomains, each subdomain resembles adistorted glucocorticoid receptor-like foldOthermetal(zinc)-bound foldOthermetal(zinc or iron)-bound fold; sequence contains two CX(n)C motifs, in mostcases n = 2Otherzinc-bound beta-ribbon motifOtherzinc-bound beta-ribbon motifOtherzinc-bound alpha + beta motifOtherdimetal(zinc)-bound alpha + beta motif; structurally diverseOtherzinc-bound alpha + beta motifOthermetal(iron)-bound foldOthermetal(zinc)-bound alpha + beta foldOthermetal(zinc)-bound alpha + beta foldOtherdimetal(zinc)-bound alpha + beta foldOtherdimetal(zinc)-bound alpha + beta foldOthermetal(zinc)-bound alpha + beta foldOthermetal(zinc)-bound alpha + beta foldOthermetal(zinc)-bound alpha + beta foldOtherZn-binding, all-alpha foldOtherall-alpha fold; Zn-binding sites are in the loops connecting helicesOtheralpha-helical fold with two Zn-binding sitesOthermetal(zinc)-bound extended beta-hairpin foldOthermetal(zinc)-bound foldOthermetal(zinc)-bound foldOthermetal(calcium)-bound fold
Terms used in Table 1 will be apparent to the skilled artisan. However, the following definitions are provided for clarity below.
“Meander” is a simple topology of a beta-sheet where any two consecutive strands are adjacent and antiparallel.
“Up-and-down” is the simplest topology for a helical bundle or folded leaf, in which consecutive helices are adjacent and antiparallel; it is approximately equivalent to the meander topology of a beta-sheet.
“Crossover connection” links secondary structures at the opposite ends of the structural core and goes across the surface of the domain.
“Greek-key” is a topology for a small number of beta sheet strands in which some interstrand connections going across the end of barrel or, in a sandwich fold, between beta sheets.
“Jelly-roll” is a variant of Greek key topology with both ends of a sandwich or a barrel fold being crossed by two interstrand connections.
“All-alpha” class has the number of secondary structures in the domain or common core described as 3-, 4-, 5-, 6- or multi-helical.
“Bundle” is an array of alpha-helices each oriented roughly along the same (bundle) axis. It may have twist, left-handed if each helix makes a positive angle to the bundle axis, or be right-handed if each helix makes a negative angle to the bundle axis.
“Folded leaf” is a layer of alpha-helices wrapped around a single hydrophobic core but not with the simple geometry of a bundle.
“Array” (of hairpins) is an assembly of alpha-helices that can not be described as a bundle or a folded leaf.
“Closed”, “partly opened” and “opened” for all-alpha structures describes the extent in which the hydrophobic core is screened by the comprising alpha-helices. “Opened” means that there is space for at least one more helix to be easily attached to the core.
Beta-sheets can be “antiparallel” (i.e. the strand direction in any two adjacent strands are antiparallel), “parallel” (all strands are parallel each other) or “mixed” (there is one strand at least that is parallel to one of its two neighbours and antiparallel to the other).
“All-beta” class includes two major fold groups: sandwiches and barrels. The “sandwich” folds are made of two beta-sheets which are usually twisted and pack so their strands are aligned. The “barrel” fold are made of single beta-sheet that twists and coils upon itself so, in most cases, the first strand in the beta sheet hydrogen bond to the last strand. The strand directions in the two opposite sides of a barrel fold are roughly orthogonal. Orthogonal packing of sheets is also seen in a few special cases of sandwich folds
“Barrel structures” are usually closed by main-chain hydrogen bonds between the first and last strands of the beta sheet, in this case it is defined by the two integer numbers: the number of strand in the beta sheet, n, and a measure of the extent the extent to which the strands in the sheet are staggered the shear number, S.
“Partly open barrel” has the edge strands not properly hydrogen bonded because one of the strands is in two parts connected with a linker of more than one residue. These edge strands can be treated as a single but interrupted strand, allowing classification with the effective strand and shear numbers, n* and S*. In the few open barrels the beta sheets are connected by only a few side-chain hydrogen bonds between the edge strands.
It is likely that there exists a bias in nature towards particular folds, simply because of the evolutionary constraints applied to protein structure and function determination. For example, approximately 30% of folds and 50% of protein superfamilies are contained within about 4-5 architectures, in particular αβ-sandwiches (two- and three-layer), αβ-barrel, β-barrel, α-updown structures (see Orengo et al., Ann. Rev. Biochem. 74, 867-900, 2005). Many folds are also reported as sharing common structural motifs due to the recurrence of simple structural motifs e.g., αβ-motifs, ββ-motifs, split βαβ-motifs. Nearly 80 different folds are classified as adopting a three-layer αβ-sandwich architecture, and the most highly-populated fold groups adopt regular architectures (e.g., TIM barrel fold, αβ-barrel, Rossman fold; three-layer, αβ-sandwich; αβ-plait, two-layer αβ-sandwich) that may be more stable when mutated (Orengo et al., ibid.). Recent statistical analyses suggest that more highly-represented folds i.e., “superfolds” support a much broader repertoire of primary sequences than other folds (Shakhnovich et al., J. Mol. Biol. 326, 1-9, 2003). For example, the CATH database provides a hierarchical classification of domains, within protein structures, in the Protein Data Bank (PDB; Berman et al., Nucl. Acids Res. 28, 235-242, 2000). There are about 32 architectures described in the CATH database.
5. Peptide Sources
Methods for producing libraries encoding peptides that correspond to naturally-occurring protein domains and/or sub-domains and/or are capable of forming secondary and/or super-secondary structures are known e.g., as described in International Patent Publication Nos. WO/2004/074479 (International Application No. PCT/AU2004/000214) and WO/2007/097923 (International Application No. PCT/AU2007/097923). The contents of these applications are incorporated herein in their entirety.
For example, nucleic acid fragments comprising genomic DNA, cDNA, or amplified nucleic acid derived from one or two or more well-characterized genomes e.g., a prokaryote genome or a eukaryote having a small genome such as a protist, dinoflagellate, alga, plant, fungus, mould, invertebrate or vertebrate may be employed to produce an expression library. Such nucleic acid fragments are derived, for example, from one or two or more of Aeropyrum pernix, Aquifex aeolicus, Archaeoglobus fulgidis, Bacillus subtilis, Bordetella pertussis, Borrelia burgdorferi, Chlamydia trachomatis, Escherichia coli, Haemophilus influenzae, Helicobacter pylori, Methanobacterium thermoautotrophicum, Methanococcus jannaschii, Mycoplasma pneumoniae, Neisseria meningitidis, Pseudomonas aeruginosa, Pyrococcus horikoshii, Synechocystis PCC 6803, Thermoplasma volcanium and Thermotoga maritima. The nucleic acid fragments are generated using art-recognized methods e.g., mechanical shearing, digestion with a nuclease, digestion with a restriction endonuclease, amplification by polymerase chain reaction (PCR) using random oligonucleotide primers, and combinations thereof.
The nucleic acid fragments are inserted into a suitable expression vector or gene construct in operable connection with a suitable promoter for expression of an encoded peptide in each clone. One approach employs site-specific recombinases to integrate fragments comprising one or two flanking recombination sites into a plasmid vector having compatible recombination sites. Site-specific recombination systems typically comprise one or more proteins that recognize a specific recombination site sequence in a plasmid vector and in the DNA insert, cleave the nucleic acids and ligate them together via cross-over event(s). Several site-specific recombinases are known in the art e.g., the bacteriophage P1 Cre/lox system (Austin et al. Cell 25, 729-736, 1981), the R/RS recombinase system from the pSR1 plasmid of the yeast Zygosaccharomyces rouxii (Araki et al., J. Mol. Biol. 182, 191-203, 1985), the Gin/gix system of phage Mu (Maeser et al., Mol. Gen. Genet. 230, 170-176, 1991), the FLP/FRT recombinase system from the 2 micron plasmid of the yeast Saccharomyces cerevisiae (Broach et al., Cell 29, 227-234, 1982), and the Integrase from bacteriophage Lambda (Landy et al., Ann. Rev. Biochem. 58, 912-949, 1989; Landy et al., Curr. Opin. Genet. Dev. 3, 699-707, 1993; Lorbach et al., J. Mol. Biol. 296, 1175-1181, 2000; and WO 01/16345). The integrase system utilizes attachment sites (attB, attP, attL, attR) to facilitate integration of insert nucleic acid into vector, wherein attB sites recombine with attP sites in a reaction mediated by an integrase enzyme to yield attL and attR sites on resulting “entry” plasmid vectors. The DNA inserts are then mobilized into a suitable “destination” expression plasmid by recombination between attL sites and attR sites in a reaction mediated by an integrase enzyme to yield attB and attP sites.
Serine recombinase systems e.g., Sin resolvase system, are also known in the art to provide for recombination between donor and acceptor sites in DNA for cloning purposes. For example, the Mycobacterium tuberculosis prophage-like element ΦRv1 encodes a site-specific recombination system utilizing an integrase of the serine recombinase family, wherein recombination occurs between a putative attP site and the host chromosome, but is unusual in that the attB site lies within a redundant repetitive element (REP13E12) of which there are seven copies in the M. tuberculosis genome; and wherein four of these repetitive elements contain attB sites suitable for ΦRv1 integration in vivo. Although the mechanism of directional control of large serine integrases is poorly understood, a recombination directionality factor (RDF) has been identified that is required for ΦRv1 integrase-mediated excisive recombination in vivo. Defined in vitro recombination reactions for both ΦRv1 integrase-mediated integration and excision require the ΦRv1 RDF for excision, but not DNA supercoiling, host factors, or high-energy cofactors (unlike the lambda integrase system). Integration, excision and excise-mediated inhibition of integration require simple substrates sites, indicating that the control of directionality does not involve the manipulation of higher-order protein-DNA architectures as described for the tyrosine integrases.
Generally, the construct used for expression is determined by the system(s) that will be used to display the encoded peptides for screening purposes e.g., by direct display on a physical medium or by phage display or recombinant expression. Such display generally provides for the peptides to assume a secondary or super-secondary structure.
Alternatively, peptide libraries are produced based on source data comprising annotations of primary sequences determined and/or predicted structures for proteins from which the component peptides are derived. For example, source data consisting of protein sequence resources such as PRINTS, Pfam, SMART, Propom, InterPro, TIGRFAMs, ADDA, CHOP, ProtoNet, SYSTERS, iProClass, SWISSPROT, COG/KOG, and protein structure family resources such as CAMPASS (Cambridge University, UK), CATH database (University College, London, UK), CE (SDSC, La Jolla, Calif., USA), DHS (University College, London, UK), ENTREZ/MMDB (NCBI, Bethesda Md., USA), Structural Classification of Protein Database (SCOP) (Andreeva et al., Nucl. Acid Res. 32:D226-D229, 2004), or the Protein Data Bank (PDB) (Berman et al., Nucleic Acid Res. 28: 235, 2000) are used to determine amino acid sequences capable of independently-forming secondary structures and/or assemblies of secondary structures and/or folds suitable for practical application in drug screening. In such an approach, synthetic peptides are produced having the sequences that are capable of forming those secondary structures and super-secondary structures, or alternatively, nucleic acid encoding the amino acid sequences are synthesized and cloned into suitable expression vectors as described herein above. As with libraries produced from genomic fragments, peptide libraries produced using bioinformatics data must be displayed for the purposes of screening to ascertain their bioactivity. Again, display generally provides for the peptides to assume a secondary or super-secondary structure.
In the foregoing methods, each clone of the library encodes, on average, a monomeric peptide.
Suitable display methods for peptide libraries include e.g., arraying the peptides on a solid surface, e.g., a microarray, or on a plurality of solid surfaces, e.g., a plurality of beads, or in microwells. The peptides may be synthesized directly onto a solid surface or immobilized on a solid surface. For example, a parallel array or pool of peptides can be produced by synthetic means and arrayed in a multi-well plate for high-throughput screening. Peptides can also be displayed using recombinant means e.g., by virtue of being expressed on the surface of a phage or a cell or by ribosome display or by in vitro display or within cells. In such methods, peptides are generally displayed (and subsequently screened) as monomers.
Modulators of CD40/CD40L Signaling
Monoclonal antibodies that block the interaction of CD40L with its cognate CD40 receptor to prevent allograft rejection in primates have been described e.g., Kirk et al., Nature Med. 5, 686-693 (1999). Such immunotherapy has also been reported for therapy of animal models of diabetes e.g., Kover et al., Diabetes 49, 1666-1670 (2000) and atherosclerosis e.g., Mach et al., Nature 394, 200-203 (1998). CD40L immunotherapy carries a high incidence of adverse consequences such as thromboembolic complications e.g., Boumpas et al., Arthrtitis Rheum. 48, 719-727 (2003), possibly due to the induction of Fc-mediated platelet aggregation e.g., Langer et al., Thromb Haemost 93, 1137-1146 (2005); Mirabet et al., Mol. Immunol. 45, 937-944 (2008).
A peptide derived from the native CD40-CD40L interface i.e., residues 181-205 of CD40L and a retro-inverso peptide analog thereof are described by Allen et al., J. Peptide Res. 65, 591-604 (2005). The term “native interface” or “native CD40-CD40L interface” or similar means that the peptide comprises a linear sequence of one of the binding partners i.e., CD40 or CD40L that is involved in their interaction, or a reverse sequence thereof e.g., a sequence of a retro-inverted analog. For example, the peptide described by Allen et al. (2005) comprises R203 of CD40L known to be involved in binding to CD40 and flanking sequence. The peptide and its chiral analog were reported to block T-cell proliferation in vitro, and to reduce incidence and severity of experimental encephalomyelitis (EAE) when administered to mice. There are a limited number of primary or secondary or tertiary structure permutations derivable the native interaction interface of CD40 and CD40L, thereby limiting the range of available therapeutics for ameliorating the adverse consequences of CD40-signaling through CD40L.
More recently, phage-expressed 7-mer peptide aptamers that had been disulfide-constrained by cyclization through their N-terminal and C-terminal cysteine residues, have also been described to bind to CD40L in vitro, and a single peptide thereof shown to inhibit CD40-mediated B-cell activation, Ig switching, endothelial cell migration and angiogenesis e.g., Deambrosis et al., J. Mol. Med. 87, 181-197 (2009). As with strategies for peptidomimetics based on the native CD40-CD40L interface, strategies employing disulfide-constrained aptamers of fixed length form a limited number of secondary or tertiary structure permutations, thereby limiting the range of available therapeutics for ameliorating the adverse consequences of CD40-signaling through CD40L. This conclusion is supported by the low primary hit rate in aptamer screens for binding activity and/or high attrition rate of aptamers tested for inhibitory activity.
There is an ongoing need for compounds that ameliorate the adverse effects of CD40L signaling events, including those events mediated by CD40 and/or Mac-1. Inverse agonists and antagonists of CD40L would be particularly useful for providing such benefits.
General
Conventional techniques of molecular biology, microbiology, virology, recombinant DNA technology, peptide synthesis in solution, solid phase peptide synthesis, and immunology are described, for example, in the following texts that are incorporated by reference:    Sambrook, Fritsch & Maniatis, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, New York, Second Edition (1989), whole of Vols I, II, and III;    DNA Cloning: A Practical Approach, Vols. I and II (D. N. Glover, ed., 1985), IRL Press, Oxford, whole of text;    Oligonucleotide Synthesis: A Practical Approach (M. J. Gait, ed., 1984) IRL Press, Oxford, whole of text, and particularly the papers therein by Gait, pp 1-22; Atkinson et al., pp 35-81; Sproat et al., pp 83-115; and Wu et al., pp 135-151;    Animal Cell Culture: Practical Approach, Third Edition (John R. W. Masters, ed., 2000), ISBN 0199637970, whole of text;    Perbal, B., A Practical Guide to Molecular Cloning (1984);    Methods In Enzymology (S. Colowick and N. Kaplan, eds., Academic Press, Inc.), whole of series;    J. F. Ramalho Ortigão, “The Chemistry of Peptide Synthesis” In: Knowledge database of Access to Virtual Laboratory website (Interactiva, Germany);    Barmy, G. and Merrifield, R. B. (1979) in The Peptides (Gross, E. and Meienhofer, J. eds.), vol. 2, pp. 1-284, Academic Press, New York.    Bodanszky, M. (1984) Principles of Peptide Synthesis, Springer-Verlag, Heidelberg.    Bodanszky, M. & Bodanszky, A. (1984) The Practice of Peptide Synthesis, Springer-Verlag, Heidelberg.    Bodanszky, M. (1985) Int. J. Peptide Protein Res. 25, 449-474.    Golemis (2002) Protein-Protein Interactions: A Molecular Cloning Manual (Illustrated), Cold Spring Harbor Laboratory, New York, ISBN 0879696281.    Smith et al., (2002) Short Protocols in Molecular Biology: A Compendium of Methods from Current Protocols in Molecular Biology, 5th Edition (Illustrated), John Wiley & Sons Inc., ISBN 0471250929.    Sambrook and Russell (2001) Molecular Cloning, Cold Spring Harbor Laboratory, New York, ISBN 0879695773.